It would have to be exceptionally balanced in the sense that putting points in skill A = the same (or similar) amount of damage/mitigation/special effect as skill B.

Blade & Soul did this reasonably well.

Unfortunately most games don't do it well, and you end up having a standard skill build that is optimal which equates to the illusion that there is customization but really there isn't.. It also can't be insanely impactful - otherwise becomes far too difficult to balance.

The closest thing to skill customization I can ever see working in this game is something we already have - equip a different weapon and boom! suddenly you have a completely different skill tree.